This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see PharmacoGx.
Bioconductor version: 3.13
Contains a set of functions to perform large-scale analysis of pharmaco-genomic data. These include the PharmacoSet object for storing the results of pharmacogenomic experiments, as well as a number of functions for computing common summaries of drug-dose response and correlating them with the molecular features in a cancer cell-line.
Author: Petr Smirnov [aut], Zhaleh Safikhani [aut], Christopher Eeles [aut], Mark Freeman [aut], Benjamin Haibe-Kains [aut, cre]
Maintainer: Benjamin Haibe-Kains <benjamin.haibe.kains at utoronto.ca>
Citation (from within R,
enter citation("PharmacoGx")
):
To install this package, start R (version "4.1") and enter:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("PharmacoGx")
For older versions of R, please refer to the appropriate Bioconductor release.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("PharmacoGx")
R Script | Creating a PharmacoSet Object | |
R Script | PharmacoGx: An R Package for Analysis of Large Pharmacogenomic Datasets | |
Reference Manual | ||
Text | NEWS |
biocViews | Classification, GeneExpression, Pharmacogenetics, Pharmacogenomics, Software |
Version | 2.4.0 |
In Bioconductor since | BioC 3.4 (R-3.3) (5 years) |
License | Artistic-2.0 |
Depends | R (>= 3.6), CoreGx |
Imports | BiocGenerics, Biobase, S4Vectors, SummarizedExperiment, MultiAssayExperiment, BiocParallel, ggplot2, magicaxis, RColorBrewer, parallel, caTools, methods, downloader, stats, utils, graphics, grDevices, reshape2, jsonlite, data.table, glue |
LinkingTo | |
Suggests | pander, rmarkdown, knitr, knitcitations, crayon, testthat, markdown |
SystemRequirements | |
Enhances | |
URL | |
BugReports | https://github.com/bhklab/PharmacoGx/issues |
Depends On Me | |
Imports Me | Xeva |
Suggests Me | ToxicoGx |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | PharmacoGx_2.4.0.tar.gz |
Windows Binary | PharmacoGx_2.4.0.zip |
macOS 10.13 (High Sierra) | PharmacoGx_2.4.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/PharmacoGx |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/PharmacoGx |
Package Short Url | https://bioconductor.org/packages/PharmacoGx/ |
Package Downloads Report | Download Stats |
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